Single-strand break repair (SSBR) is an important sub-pathway of BER. Studies have revealed a genetic link between defects in components of SSBR aprataxin, tyrosyl-DNA phosphodiesterase 1, DNA polynucleotide kinase phosphatase and most recently x-ray cross-complementing protein 1 (XRCC1) and human neurological disease, implicating this repair mechanism in protection against neuronal cell loss and the maintenance of brain function. Ataxia with oculomotor apraxia 1 (AOA1) is caused by mutation in the APTX gene, which encodes the stand break repair protein aprataxin, an enzyme that removes 5-adenylate groups in DNA that arise from aborted ligation reactions. AOA1 is characterized by global cerebellar atrophy, highlighted by loss of Purkinje cells, ocular motor apraxia, and motor and sensory neuropathy. Notably, AOA1 patients lack the cancer susceptibility and other peripheral symptoms (e.g., immunological deficiencies) commonly associated with other inherited disorders stemming from a DNA repair defect. We have previously reported that aprataxin activity is necessary for maintaining optimal mitochondrial function, indicating that there is likely a mitochondrial component to the disease phenotype of AOA1. In a separate study, we have found that deficiency in a key SSBR/BER protein, i.e., XRCC1, is a risk factor for cellular damage caused by ischemic brain injury and impairs recovery following stroke induction. Additional work has revealed that a modest decrement in SSBR/BER capacity, via polymerase haploinsufficiency, can render the brain more vulnerable to Alzheimer Disease (AD)-related molecular and cellular alterations. Lastly, our data indicate that because of their higher BER capacity, proliferative neural progenitor cells are more efficient at repairing DNA damage compared with their neuronally differentiated progeny, perhaps increasing the vulnerability of neurons to oxidative stress. Current work is focusing on the role of XRCC1 in maintaining mitochondrial function and preserving skeletal muscle integrity during development and in adulthood using a collection of cell and mouse models. Expansion of CAG/CTG repeats in DNA is the underlying cause of >14 genetic disorders, including Huntington disease (HD) and myotonic dystrophy. The mutational process is ongoing, with increases in repeat size enhancing the toxicity of the expansion in specific tissues. In many repeat diseases, the repeats exhibit high instability in the striatum, whereas instability is minimal in the cerebellum. In our past work, using defined DNA repair assays, we have provided molecular insights into how the tissue-selective instability of CAG/CTG repeats may arise. In particular, our results showed that the BER protein stoichiometry, overall nucleotide sequence, and DNA damage position can modulate repair outcome and that a suboptimal long-patch BER activity promotes CAG/CTG repeat instability. Moreover, we have found that the BER DNA glycosylase NEIL1 contributes to germline and somatic CAG repeat expansion in HD and that the binding and strand incision efficiency of the major human abasic endonuclease, APE1, is influenced by domain sequence, conformation, AP site location/relative positioning and duplex thermodynamic stability. Our results have both predictive and mechanistic implications for the success and failure of repair protein activity at such oxidatively sensitive, conformationally plastic/dynamic repetitive DNA domains. Cockayne Syndrome (CS) is an autosomal recessive disorder, characterized by growth failure, neurological abnormalities, premature aging symptoms, and cutaneous photosensitivity, but no increased cancer incidence. CS is divided into two major complementation groups: CSA (mutation in CKN1) and CSB (mutation in ERCC6). Of the patients suffering from CS, 80% have mutations in the CSB gene. Our past work has helped define the biochemical properties of CSB, revealing that the protein interacts with a diverse range of nucleic acid substrates and likely has important ATP-dependent and ATP-independent functions in DNA and/or RNA metabolism. Furthermore, results, obtained in collaboration with Dr. Vilhelm Bohr, suggest that CSB contributes to both nuclear and mitochondrial BER, and may act as a mitochondrial DNA damage sensor, inducing mitochondrial autophagy in response to stress. More recently, it has come to light that much of the mitochondrial dysfunction observed in CS may arise indirectly, whereby defects in nuclear DNA processing result in hyperactivation of poly(ADP-ribose) polymerase 1 (PARP1), depletion of its co-substrate nicatinamide (NAD+), and consequent mitochondrial defects. Thus, a majority of the current research has focused on identifying the major nuclear DNA substrates of the CS proteins. Some of the recent work supports a role for impaired ribosomal DNA transcription in CS and suggests that transcription-coupled resolution of secondary structures (G-quadruplexes) may be a mechanism to repress spurious activation of the DNA damage response. In light of our observation that the CSB protein interacts with the 5 to 3 exonuclease, SNM1A, which has documented roles in the repair of DNA ICLs, we are pursuing the hypothesis that deficiencies in the repair of endogenous transcription-blocking lesions underlie disease manifestation. Besides ICLs, such modifications could include bulky oxidative lesions, such as cyclopurines, as well as potentially DNA double-strand breaks (DSBs). In line with our hypothesis, we have found in laser microirradiation-confocal microscopy experiments that both CSA and CSB respond most robustly (in terms of kinetics and accumulation) to complex DNA damage, with ICLs > DSBs > bulky monoadducts > simple oxidative lesions. Notably, we were unable to see a convincing recruitment of CSA to sites of simple oxidative DNA damage, implying that BER lesions are not the primary substrates of the CS protein response. Using Caenorhabditis elegans mutants, we have identified DNA repair factors that protect against the genotoxicity of ICLs generated by trioxsalen/ultraviolet A (TMP/UVA) during development and aging. Mutations in nucleotide excision repair (NER) components (e.g., XPA-1 and XPF-1) imparted extreme sensitivity to TMP/UVA relative to wild-type animals, manifested as developmental arrest, defects in adult tissue morphology and functionality, and shortened lifespan. Moreover, compensatory roles for global-genome (XPC-1) and transcription-coupled (CSB-1) NER in ICL sensing were observed. Our work therefore supports both replication-dependent and -independent ICL repair networks, and establishes nematodes as a model for investigating the repair and consequences of DNA crosslinks in metazoan development and in adult post-mitotic and proliferative germ cells. A major focus of the ongoing work at present is to thoroughly define the molecular choreography of the emerging transcription-associated ICL repair response, and how it might engage both CSA and CSB.